Vol. 17 No. 2, October 2016
Accredited by the Indonesian Institute of
Sciences No. 818/E/2015
Editorial Board
Editor-in-Chief
Markus Anda Mineralogy and Soil Classification (Scopus ID : 23024287000 / h-Index: 6)
Indonesian Center for Agricultural Land Resources Research and Development,
Indonesia
International Editorial Board
Supriadi Plant Pathology, Indonesian Spice and Medicinal Crops Research Institute,
Indonesia
Budi Tangendjaja Animal Feed and Nutrition, (Scopus ID: 6508321607 / h-Index : 6) Indonesian
Center for Animal Research and Development, Indonesia
Dewa Ketut Sadra Swastika Socioeconomics, Indonesian Center for Agricultural Socio Economic and Policy
Studies, Indonesia
Randy Alan Dahlgren Soil Science and Biogeochemistry, (Scopus ID: 7005899511 / h-Index : 45)
University of California, Davis, United States
Bunyamin Tar'an Plant Biotechnology, (Scopus ID: 56181765200 / h-Index : 17) University of
Saskatchewan, Canada
Soon-Wook Kwan Plant Breeding and Molecular Breeding, (Scopus ID : 55782595000 / h-Index
: 9) Pusan National University, Republic of Korea
Sri Yuliani Postharvest Technology, (Scopus ID : 9844293200 / h-Index : 6) Indonesian
Center for Agricultural Postharvest Research and Development, Indonesia
I Made Tasma Plant Breeding and Molecular Biology, (Scopus ID : 6507936762 / h-Index : 6)Indonesian Center for Agricultural Biotechnology and Genetic Resources
Research and Development, Indonesia
Puji Lestari Molecular Biology, (Scopus ID : 6507413576 / h-Index : 6) Indonesian
Center for Agricultural Biotechnology and Genetic Resources Research and
Development, Indonesia
Md. Babul Akter Crop Physiology and Molecular Breeding, Bangladesh Institute of Nuclear
Agriculture (BINA), Bangladesh
Assistant Editor
Endang Setyorini Indonesian Center for Agricultural Library and Technology Dissemination,
Indonesia
Slamet Sutriswanto Indonesian Center for Agricultural Library and Technology Dissemination,
Indonesia
Layout Editor
Ujang Sahali Indonesian Center for Agricultural Library and Technology Dissemination,
Indonesia
All inquiries and manuscripts should be sent to the:
The editorial office
Indonesian Center for Agricultural Library and Technology Dissemination
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Website : http://pustaka.litbang.pertanian.go.id; http://ejurnal.litbang.pertanian.go.id/index.php/ijas
Printed in Indonesia
2016, Indonesian Agency for Agricultural Research and Development, Jakarta, Indonesia
ISSN 1411-982X
E-ISSN 2354-8509
SCIENCE
Indonesian Journal of
AGRICULTURAL
International Peer-Reviewer
Kularb Laosatit Genetic and Molecular Biology, (Scopus ID : 36872678000 / h-Index : 3), Faculty
of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen,
Nakhon Pathom, 73140, Thailand
Ahmad Kurnain Soil Science, (Scopus ID : 56515310300 / h-Index: -), Lambung Mangkurat
University, Banjarmasin, Indonesia
Purwiyatno Hariyadi Postharvest, (Scopus ID : 16156219500 / h-Index : 6) Bogor Agricultural
University, Indonesia
Ika Mariska Plant Physiology and Biotechnology, (Scopus ID : 6507460259 / h Index : 4)
Indonesian Center for Agricultural Biotechnology and Genetic
Resources Research and Development, Indonesia
Backki Kim Biochemistry, Genetics and Molecular Biology, (Scopus ID : 56042253700 /
h-Index : 3), Texas A&M University, College Station, TX 77843, United States
Sutoro Agronomy, Indonesian Center for Agricultural Biotechnology and Genetic
Resources Research and Development, Indonesia
Production and quality enhancement of mango using fan jet
sprayer irrigation technique
Nani Heryani, Budi Kartiwa, Yayan Apriyana and Haris Syahbuddin 41–48
Agrobacterium tumefaciens-mediated in-planta transformation
of Indonesian maize using plG121Hm-Cs plasmid containing nptII
and hpt genes
Edy Listanto, Eny Ida Riyanti and Sustiprijatno 49–56
Genomic variation of five Indonesian cacao (Theobroma cacao L.)
varieties based on analysis using next generation sequencing
I Made Tasma, Dani Satyawan, Habib Rijzaani, Ida Rosdianti,
Puji Lestari and Rubiyo 57–64
The potential use of SSR markers to support the morphological
identification of Indonesian mungbean varieties
Reflinur, Puji Lestari and Suk-Ha Lee 65–74
Capillary water rise in peat soil as affected by various
groundwater levels
Muhammad Imam Nugraha, Wahida Annisa, Lailan Syaufina
and Syaiful Anwar 75–83
Indonesian Journal of Agricultural Science is previously published as Indonesian Journal of Crop Science (1985 - 1999). This
journal is published in one volume of two issues per year by the Indonesian Agency for Agricultural Research and Development.
It is available online at: ejurnal.litbang.pertanian.go.id/index.php/ijas
The journal publishes primary research articles from any source if they make a significant original contribution to the experimental
or theoretical understanding of some aspect of agricultural science in Indonesia. The definition of agricultural science is kept as
wide as possible to allow the broadest coverage in the journal.
ISSN 1411-982X
E-ISSN 2354-8509
Vol. 17 No. 2, October 2016
SCIENCE
Indonesian Journal of
AGRICULTURAL
CONTENTS
UDC: 631.87
Wahida Annisa and Dedi Nursyamsi (Indonesian Swampland
Agricultural Research Institute, Banjarbaru)
Iron Dynamics and Its Relation to Soil Redox Potential and
Plant Growth in Acid Sulphate Soil of South Kalimantan,
Indonesia (Orig. Eng.)
IJAS, April 2016, vol. 17 no. 1, p. 1–8, 1 tab., 8 ill., 27 ref.
Organic matter has a function to maintain reductive
conditions and to chelate toxic elements in acid sulphate soils.
The study aimed to assess the dynamics of ferrous iron (Fe2+)
in acid sulphate soil and its correlation with soil redox
potential (Eh) and plant growth. The experiment was arranged
in two factorial randomized block design with three
replications. The first factor was two types of organic matter:
(1) control (without organic matter), (2) rice straw and (3)
rush weed (Eleocharis dulcis). The second factor was time of
decomposition of organic matter: I1 = 2 weeks, I
2 = 4 weeks, I
3
= 8 weeks, and I4
= 12 weeks (farmer practice). The results
showed that concentration of ferrous iron in the soil ranged
from 782 to 1308 mg kg-1 during the rice growing season. The
highest constant rate of iron reduction (k F2+) was observed on
application of rice straw and rush weed with decomposition
time of 8 weeks with the k Fe2+ value of 0.016 and 0.011 per
day, respectively, while the ferrous iron formation without
organic matter had the k Fe2+ value of 0.077 per day. The
ferric iron (Fe3+) reduction served as a function of soil Eh as
indicated by the negative correlation of ferrous iron and Eh (r
= -0.856*). Organic matter decreased exchangeable iron due
to chelating reaction. Iron concentration in roots was
negatively correlated with soil soluble iron (r = -0.62*).
Application of rice straw decomposed for 8 weeks increased
the height of rice plant up to 105.67 cm. The score of Fe2+
toxicity at 8 weeks after planting ranged from 2 to 3, so rice
crop did not show iron toxicity symptoms.
(Author)
Keywords: Ferrous iron, redox potential, plant growth, acid
sulphate soil
————————————————————————UDC: 634.471.1-18
Yosi Zendra Jonia, Riry Prihatinia, Darda Efendib and Ika
Roostikac (aIndonesian Tropical Fruit Research Institute,
Solok, bDepartment of Agronomy and Horticulture, Bogor
Agricultural University, Bogor, cIndonesian Center for
Agricultural Biotechnology and Genetic Resources Research
and Development, Bogor)
Effect of Different Sources of Plant Growth Regulator on The
Induction and Development of Mangosteen Somatic Embryos
(Orig. Eng.)
IJAS, April 2016, vol. 17 no. 1, p. 9–16, 1 tab., 9 ill., 26 ref.
Somatic embryogenesis is a technique for regenerating
embryos derived from somatic cells of various plant species.
This technique along with the utilization of plant growth
regulator (PGR) might benefit for mass propagation and
improvement of plant species through biotechnological tools.
The study aimed to determine the effect of different plant
growth regu-lators, namely 6-benzyladenine (BA) and
thidiazuron (TDZ) on the embryogenic callus induction as well
as casein hydrolysate and malt extract on the somatic embryo
development of mangosteen. The explants used were in vitro
young stems of mangosteen clone Leuwiliang. This study
consisted of two experiments, namely induction of
embryogenic callus and formation of somatic embryo. The
first experiment was arranged as factorial in a completely
randomized design with BA (0 and 0.7 mg l-1) as the first factor
and TDZ (0, 0.1, 0.5 and 1.0 mg l -1) as the second factor. The
second experiment consisted of four treatments, i.e. casein
hydrolysate and malt extract at the rate of 500 and 1,000 mg
l-1. The results showed that the best medium for embryogenic
callus induction was MS supplemented with 0.1 mg l-1 TDZ,
which resulted semifriable calli. Casein hydrolysate and malt
extract could not induce the formation of somatic embryos.
After two times subcultures on the same MS medium
supplemented with 0.5 mg l-1 TDZ and 0.7 mg l-1 BA, a total of
33.8 somatic embryos per explant was induced. The successful
somatic embryogenesis would support mangosteen breeding
and in vitro mass propagation program.
(Author)
Keywords: Garcinia mangostana, plant growth regulator,
callus induction, somatic embryo
————————————————————————UDC: 635.356-152
Nur Kholilatul Izzaha, Reflinurb and Tae-Jin Yangc (aIndonesian
Industrial and Beverage Crops Research Institute, Pakuwon,
Sukabumi, bIndonesian Center of Agricultural Biotechnology
and Genetic Resources Research and Development, Bogor,cDepartment of Plant Science and Research Institute for
Agriculture and Life Sciences, Seoul National University
Seoul)
Development of EST-SSR Markers to Assess Genetic Diversity
of Broccoli and Its Related Species (Orig. Eng.)
IJAS, April 2016, vol. 17 no. 1, p. 17–26, 5 tab., 4 ill., 31 ref.
Development of Expressed Sequence Tag-Simple Sequence
Repeat (EST-SSR) markers derived from public database is
known to be more efficient, faster and low cost. The objective
of this study was to generate a new set of EST-SSR markers for
broccoli and its related species and their usefulness for
assessing their genetic diversity. A total of 202 Brassica
oleracea ESTs were retrieved from NCBI and then assembled
into 172 unigenes by means of CAP3 program. Identification
INDONESIAN JOURNAL OF AGRICULTURAL SCIENCE
ISSN 1411-982X (printed version) Volume 17, 2016
E-ISSN 2354-8509 (electronic version)
The descriptons given are free terms. This abstract sheets may be reproduced without permission or charge.
of SSRs was carried out using web-based tool, RepeatMasker
software. Afterwards, EST-SSR markers were developed using
Primer3 program. Among the identified SSRs, trinucleotide
repeats were the most common repeat types, which accounted
for about 50%. A total of eight primer pairs were successfully
designed and yielded amplification products. Among them, five
markers were polymorphic and displayed a total of 30 alleles
with an average number of six alleles per locus. The
polymorphic markers were subsequently used for analyzing
genetic diversity of 36 B. oleracea cultivars including 22
broccoli, five cauliflower and nine kohlrabi cultivars based on
genetic similarity matrix as implemented in NTSYS program.
At similarity coefficient of 61%, a UPGMA clustering
dendrogram effectively separated 36 genotypes into three
main groups, where 30 out of 36 genotypes were clearly
discriminated. The result obtained in the present study would
help breeders in selecting parental lines for crossing.
Moreover, the novel EST-SSR markers developed in the study
could be a valuable tool for differentiating cultivars of broccoli
and related species.
(Author)
Keywords: Broccoli, cauliflower, kohlrabi, EST-SSR markers,
genetic diversity
————————————————————————UDC: 634.773+635.965.274
Riry Prihatinia and Norihan Mohamad Salehb (aIndonesian
Tropical Fruit Research Institute, Solok, bDepartment Cell and
Molecular Biology, Faculty of Biotechnology and
Biomolecular Sciences, Universiti Putra Malaysia 43400 UPM
Serdang Selangor DE)
Sensitivity of Pigment Content of Banana and Orchid Tissue
Culture Exposed to Extremely Low Frequency
Electromagnetic Field (Orig. Eng.)
IJAS, April 2016, vol. 17 no. 1, p. 27–34, 1 tab., 2 ill., 38 ref.
Natural exposure of extremely low frequency electromagnetic
field (ELF-EMF) occurs in the environment and acts as one of
the abiotic factors that affect the growth and development of
organisms. This study was conducted to determine the effect
of ELF-EMF on the tissue cultured banana and slipper orchid
chlorophyll content as one of the indicators in measuring
plant photosynthetic capacity. Four days old banana (Musa sp.
cv. Berangan) corm and seven days old slipper orchid
(Paphiopedilum rothschildianum) cultures were exposed to 6
and 12 mT ELF-EMF generated by controllable ELF-EMF
built up machine for 0.5, 1, 2 and 4 hours. After exposure, the
banana and orchid cultures were incubated at 25° C for 8 and 16
weeks, respectively. The results showed that the ELF-EMF
exposure had different effects on banana and slipper orchid
cultures though both plant species belong to monocotyledon.
The highest increase in chlorophyll content on banana was
resulted by the high intensity and long duration of ELF-EMF
exposure (12 mT for 4 hours), whereas on slipper orchid the
modest and short duration of ELF-EMF exposure produced the
most excessive chlorophyll content. Different ELF-EMF
exposures (12 mT for 4 hours and 6 mT for 30 minutes) had
potential to be applied on each plant to improve in vitro plant
(banana and slipper orchid, respectively) growth. The
increased chlorophyll and carotene/xanthophyll content on
banana indicated that the banana was more tolerant to ELF-
EMF exposure compared to slipper orchid.
(Author)
Keywords: Banana, orchid, carotene, chlorophyll, electro-
magnetic field
————————————————————————UDC: 633.683
Imron Riyadi and Sumaryono (Indonesian Research Institute
for Biotechnology and Bioindustry, Bogor)
Effect of gamma irradiation on the growth and development
of sago palm (Metroxylon sagu Rottb.) calli (Orig. Eng.)
IJAS, April 2016, vol. 17 no. 1, p. 35–40, 2 tab., 3 ill., 22 ref.
The application of gamma irradiation on plant materials may
increase the genetic variation of the offspring with useful
traits. The experiment was conducted to determine the effect
of irradiation dosage of gamma ray on growth and development
of sago palm (Metroxylon sagu) calli. Friable calli of sago
palm derived from suspension culture were used as a material
source. The primary calli were initiated from apical
meristematic tissues of sago palm suckers of Alitir variety
from Merauke, Papua. The treatments used were dosage of
gamma ray irradiation at 0, 5, 10, 15, 20 and 25 Gy. The
treated calli were then subcultured on modified Murashige and
Skoog (MMS) solid medium containing 3% sucrose and 0.1%
activated charcoal and added with 1 mg l-1 2,4-D and 0.1 mg l-
1 kinetin. The results showed that at all irradiation dosages,
calli biomass increased significantly. The highest proliferation
of calli biomass of 5.33 folds from the initial culture after 4
weeks was achieved at gamma irradiation of 25 Gy, whereas
the lowest proliferation of calli biomass of 3.4 folds was
achieved at control. The best development of embryogenic
calli was obtained at 10 Gy that produced 100% somatic
embryos, whereas the lowest somatic embryo formation at 0%
was obtained at 0 and 25 Gy after one subculture. High
response of somatic embryo induction to gamma irradiation at
10 Gy may increase production of somatic embryos. These
results can be used in in vitro breeding of sago palm via
mutagenesis to create new elite varieties.
(Author)
Keywords: Metroxylon sagu, gamma irradiation, embryogenic
calli, somatic embryo
————————————————————————UDC: 634.441.2-167
Nani Heryani, Budi Kartiwa, Yayan Apriyana and Haris
Syahbuddin (Indonesian Agroclimate and Hydrology Research
Institute, Bogor)
Production and Quality Enhancement of Mango Using Fan Jet
Sprayer Irrigation Technique (Orig. Eng.)
IJAS, October 2016, vol. 17 no. 2, p. 41–48, 6 tab., 4 ill., 36
ref.
Lack of water in reproductive phases (flowering, fruit
formation and maturation) of mango can reduce fruit
production and quality. In these phases the plant must be
protected from water stress. The aim of the research was to
assess the effect of irrigation on the productivity and quality
of mango fruits. The study was conducted at the Cukurgondang
Experimental Station, Pasuruan, East Java, from April to
December 2013, using 40 mango trees of 21 year-old Arum
Manis variety. Mangoes were planted on five rows with eight
plants for each row and 6 m x 6 m spacing within the row. Fan
jet sprayer irrigation was installed using hose according to
plant diameter. The irrigation technique of fan jet sprayer with
four nozzles per plant was applied at 125, 100, 75, 50 and 0%
of crop water requirements or equal to 828, 663, 497, 331 and
0 liters of water per tree, every seven days. The parameters
observed were the number and weight of fallen fruits and the
number, weight and quality of mangoes harvested. The results
showed that irrigation of 50% and 75% of crop water
requirement had the highest and lowest number of fallen fruits
(26% and 14% of total production), respectively. The highest
and lowest total number of mangoes were 3.108 and 1904
fruits, respectively, which were achieved at irrigation of 50%
and 75% of crop water requirement. Further, the highest and
lowest total weight of mango fruits were 1036.2 and 677.9 kg
respectively which were achieved at irrigation of 50% and
125% of crop water requirement. Mango fruits produced were
dominated by grades 2 and 3 with A quality.
(Author)
Keywords: Mango, production, quality, fan jet sprayer
————————————————————————
UDC: 633.15-152
Edy Listanto, Eny Ida Riyanti and Sustiprijatno (Indonesian
Center for Agricultural Biotechnology and Genetic Resources
Research and Development, Bogor)
Agrobacterium tumefaciens-Mediated In-Planta Transforma-
tion of Indonesian Maize Using plG121Hm-Cs Plasmid
Containing nptll and hpt Genes (Orig. Eng.)
IJAS October 2016, vol. 17 no. 2, p. 49–56, 1 tab., 5 ill., 33 ref.
Maize (Zea mays L.) productivity in Indonesia is challenged to
be increased using genetic engineering. Recent advances in
Agrobacterium tumefaciens-mediated in-planta transforma-
tion makes it possible to transform maize with low cost, and
simple method. This study aimed to confirm pIG121Hm-Cs
plasmid in A. tumefaciens, and to estimate the efficiency level
of A. tumefaciens-mediated in-planta transformation of
Indonesian maize by using pIG121Hm-Cs plasmid containing
nptII and hpt genes. A series of studies were conducted
including confirmation of gene construct of pIG121Hm-Cs
plasmid in A. tumefaciens, transformation of four maize lines
through A. tumefaciens-mediated in-planta technique,
acclimatization of transformant plants and molecular analysis
of selected plants using polymerase chain reaction (PCR). The
pIG121Hm-Cs plasmid was confirmed via PCR analysis using
specific primers of nptII and hpt genes and resulted 700 bp and
500 bp for fragments of nptII and hpt, respectively. After
selection, acclimatization and molecular analysis steps, the
efficiency levels of transformation of four maize lines were
low, ranging from 3.8% to 12.8%. The level of transformation
efficiency of ST-27 line was the highest accounting for 12.8%
of 45 planted embryos on selection medium based on PCR
analysis using specific primer for nptII gene. Overall, A.
tumefaciens-mediated in planta transformation on maize floral
pistil in this study proved to be successful and rapid. Therefore,
this enhanced transformation method will be beneficial for
Indonesian maize genetic engineering.
(Author)
Keywords: Maize, Agrobacterium tumefaciens, in-planta
transformation
————————————————————————UDC: 633.74-152
I Made Tasmaa, Dani Satyawana, Habib Rijzaania, Ida
Rosdiantia, Puji Lestaria and Rubiyob (aIndonesian Center for
Agricultural Biotechnology and Genetic Resources Research
and Development, Bogor, bIndonesian Industrial and Beverage
Crop Research Institute, Pakuwon)
Genomic Variation of Five Indonesian Cacao (Theobroma
cacao L.) Varieties Based on Analysis Using Next Generation
Sequencing (Orig. Eng.)
IJAS October 2016, vol. 17 no. 2, p. 57–64, 3 tab., 2 ill., 42
ref.
Indonesian cacao productivity is still low mainly due to the
lack availability of superior cacao planting materials. A new
breeding method is necessary to expedite cacao yield
improvement programs. To date, no study has yet been done
to characterize Indonesian cacao varieties at the whole
genome level. The objective of this study was to characterize
genomic variation of five superior Indonesian cacao varieties
using next-generation sequencing. Genetic materials used were
five Indonesian cacao varieties, i.e. ICCRI2, ICCRI3, ICCRI4,
SUL2 and ICS13. Genome sequences were mapped to the cacao
reference genome sequence of Criollo variety. Sequence
alignment and genomic variation discovery were done using
Bowtie2 and mpileup software of Samtools, respectively. A
total of 2,326,088 single nucleotide polymorphisms (SNPs)
and 362,081 insertions and deletions (Indels) were obtained
from this study. In average, a DNA variant was identified in
every 121 nucleotides of the genome sequence. Most of the
DNA variants were located outside the genes. Only 347,907
SNPs and Indels (13.18%) were located within protein coding
region (exon). Among the DNA variations within exon,
188,949 SNPs caused missense mutation and 1,535 SNPs
induced nonsense mutation. Unique gene-based SNPs were also
discovered from this study that can be used as fingerprints for
the particular cacao variety. The DNA variants obtained were
excellent DNA marker resources to support cacao breeding
programs. The SNPs discovered are useful as materials for
genome-wide SNP chip development to be used for gene and
QTL tagging of important traits for expediting national cacao
breeding program.
(Author)
Keywords: Theobroma cacao, genome sequencing, genome
variation, SNP, next generation sequencing
————————————————————————UDC: 633.3-152
Reflinura, Puji Lestaria and Suk-Ha-Leeb (aIndonesian Center
for Agricultural Biotechnology and Genetic Resources
Research and Development, Bogor, bDepartment of Plant
Science and Research Institute for Agriculture and Life
Sciences, Seoul National University)
The Potential Use of SSR Markers to Support the
Morphological Identification of Indonesian Mungbean
Varieties (Orig. Eng.)
IJAS, October 2016, vol. 17 no. 2, p. 65–74, 4 tab., 2 ill., 31 ref.
Mungbean varieties were mainly characterized based on
morphological traits. Molecular genetic approach is expected
to help the breeder in identification of mungbean varieties in
more detail and to protect intellectual property right. This
study aimed to identify Indonesian mungbean varieties based
on DNA fingerprint profile using a marker set to support
morphological characters. A total of 22 Indonesian mungbean
accessions were characterized based on 21 morphological traits
and 55 simple sequence repeats (SSRs) primers. Of the total 22
mungbean varieties used in the present study, 16 varieties were
improved varieties and remaining six varieties were local
varieties originated from Java, Nusa Tenggara and Sulawesi
collected in GeneBank of ICABIOGRAD. The results showed
that the 21 morphological characters were not sufficient to
differentiate 22 mungbean varieties, while SSR analysis
revealed that eight multi-alleles markers and high polymorphic
information content (PIC) values have been successfully
selected for varietal identification. The selected markers
enabled to differentiate each mungbean variety according to
their genetic marker with the lowest distance of 0.125,
demonstrating the robustness of the selected marker set as a
tool to identify a specific DNA fingerprint profile as a varietal
identity (ID). The genetic identity of a variety was shown by
digital barcoding which represented a series of alleles produced
by corresponding markers. The DNA fingerprint profile of
each variety would be beneficial as reference identities of a
mungbean variety.
(Author)
Keywords: Mungbean, morphological characters, SSR markers,
DNA fingerprint, varietal identity
————————————————————————UDC: 631.445.1
Muhammad Imam Nugrahaa, Wahida Annisab, Lailan Syaufinac
and Syaiful Anward (aGraduate Student at Bogor Agricultural
University, Bogor, bIndonesian Swampland Agricultural
Research Istitute, Banjarbaru, cFaculty of Forestry, Bogor
Agricultural University, dFaculty of Agriculture, Bogor
Agricultural University)
Capillary Water Rise in Peat Soil as Affected by Various
Groundwater Levels (Orig. Eng.)
IJAS, October 2016, vol. 17 no. 2, p. 75–83, 3 tab., 6 ill., 31 ref.
Capillary water in peatlands has a very important role in
supplying water to the root zone of plants. The current water
content in the root zone depends mainly on groundwater levels
in some areas with shallow water levels. The study aimed to
measure the capillary water dynamics in peat soils at various
soil densities and groundwater levels which were observed from
the changes in peat color, moisture distribution, water content
and hydrophobicity of peat soil. The study was conducted in
the greenhouse of Indonesian Swampland Agricultural Research
Institute, Banjarbaru, South Kalimantan. The experiment was
arranged in a randomized block design with two factors and
three replications. The first factor was the bulk density (BD)
of peat, namely BD-1 (on actual condition, 0.1 g cm-3) and
BD-2 (compressed into 0.2 g cm -3). The second factor was
simulated groundwater levels (GWL) consisting of GWL-1 (-
100 cm), GWL-2 (-70 cm) and GWL-3 (-40 cm) from soil
surfaces. The results showed that the rise of capillary water in
peat soil reached a maximum height of 50 cm which was
characterized by the increase in water content at the top layer
in the range of 105–127% for BD-1 and 141–181% for BD-2.
The highest value of water content (308%) was achieved in
the treatment of GWL-3 with BD-2 and the lowest (37%) was
in the treatment of GWL-1 with BD-1. The rate of capillary
water rose progressively corresponded to the increase in BD
value because the number of micropores of BD-2 was greater.
(Author)
Keywords: Peat soil, capillary water, groundwater level, bulk
density, water content
INDONESIAN JOURNAL OF AGRICULTURAL SCIENCE
ISSN 1411-982X (versi tercetak) Volume 17, 2016
E-ISSN 2354-8509 (versi elektronik)
Kata kunci yang dicantumkan adalah istilah bebas. Lembar abstrak ini boleh dikopi tanpa izin dan biaya.
UDC: 631.87
Wahida Annisa dan Dedi Nursyamsi (Balai Penelitian Pertanian
Lahan Rawa, Banjarbaru)
Dinamika Besi dan Hubungannya dengan Potensi Redoks
Tanah dan Pertumbuhan Tanaman di Tanah Sulfat Masam
Kalimantan Selatan, Indonesia (Orig. Eng.)
IJAS, April 2016, vol. 17 no. 1, p. 1–8, 1 tab., 8 ill., 27 ref.
Bahan organik memiliki fungsi mempertahankan kondisi
reduktif tanah dan mengkelat unsur beracun di tanah sulfat
masam. Penelitian bertujuan untuk mempelajari dinamika besi
ferro di tanah sulfat masam serta korelasinya dengan potensi
redoks (Eh) tanah dan pertumbuhan tanaman. Penelitian
menggunakan rancangan faktorial dua faktor dan diulang tiga
kali. Faktor pertama adalah jenis bahan organik, yaitu (1)
kontrol (tanpa bahan organik), (2) jerami padi, dan (3) gulma
purun (Eleocharis dulcis). Faktor kedua adalah waktu
dekomposisi bahan organik, yaitu I1 = 2 minggu, I
2 = 4 minggu,
I3 = 8 minggu, dan I
4 = 12 minggu (pola petani Banjar). Hasil
penelitian menunjukkan bahwa secara umum konsentrasi besi
ferro (Fe2+) di tanah sulfat masam berkisar 782–1308 mg kg-1
selama pertumbuhan tanaman padi. Konstanta tertinggi
kecepatan reduksi besi (k Fe2+) terdapat pada perlakuan jerami
padi dan gulma purun dengan waktu inkubasi 8 minggu, masing-
masing 0,016 dan 0,011 per hari. Sementara konstanta
terendah ditunjukkan pada perlakuan tanpa bahan organik,
yakni 0,077 per hari. Reduksi besi ferri (Fe3+) merupakan
fungsi dari nilai Eh tanah yang ditunjukkan dengan adanya
korelasi negatif antara besi ferro dan nilai Eh dengan r = -
0,856*. Bahan organik dapat menurunkan konsentrasi besi
tukar dalam tanah melalui pengkelatan. Terdapat korelasi
negatif antara konsentrasi besi dalam akar dengan yang larut
dalam tanah dengan nilai r = -0.62*. Pemberian kompos jerami
padi dengan waktu inkubasi 8 minggu meningkatkan tinggi
tanaman padi yang mencapai 105,67 cm. Nilai skor keracunan
besi pada tanaman pada umur 8 minggu setelah tanam berkisar
2–3 dan disimpulkan tanaman padi cukup toleran di lahan
sulfat masam karena tidak menunjukkan gejala keracunan besi.
(Penulis)
Kata kunci: Besi ferro, potensial redoks, pertumbuhan tanaman,
tanah sulfat masam
————————————————————————UDC: 634.471.1-18
Yosi Zendra Jonia, Riry Prihatinia, Darda Efendib dan Ika
Roostikac (aBalai Penelitian Tanaman Buah Tropika, Solok,bDepartemen Agronomi dan Hortikultura, Institut Pertanian
Bogor, Bogor, cBalai Besar Penelitian dan Pengembangan
Bioteknologi dan Sumberdaya Genetik Pertanian, Bogor)
Pengaruh Sumber Zat Pengatur Tumbuh Tanaman yang
Berbeda pada Induksi dan Pengembangan Embrio Somatik
Manggis (Orig. Eng.)
IJAS, April 2016, vol. 17 no. 1, p. 9–16, 1 tab., 9 ill., 26 ref.
Embriogenesis somatik merupakan proses pembentukan
embrio dari sel somatik pada berbagai spesies tanaman. Teknik
ini bermanfaat untuk perbanyakan benih tanaman secara
massal dan perbaikan bahan tanaman dengan teknik rekayasa
genetik. Penelitian bertujuan untuk mengetahui pengaruh
beberapa zat pengatur tumbuh tanaman, yakni 6-bensiladenin
(BA) dan thidiazuron (TDZ) terhadap induksi kalus
embriogenik serta kasein hidrolisat dan ekstrak malt terhadap
pembentukan embrio somatik manggis. Eksplan yang
digunakan adalah batang muda in vitro manggis klon
Leuwiliang. Penelitian terdiri atas dua percobaan, yaitu induksi
kalus embriogenik dan pembentukan embrio somatik.
Percobaan induksi kalus embriogenik disusun secara faktorial
dalam rancangan acak lengkap. Faktor pertama adalah BA (0
dan 0,7 mg l-1) dan faktor kedua adalah TDZ (0; 0,1; 0,5 dan
1,0 mg l-1). Percobaan pembentukan embrio somatik terdiri
atas perlakuan kasein hidrolisat (500 dan 1.000 mg l-1) dan
ekstrak malt (500 dan 1.000 mg l-1). Hasil penelitian
menunjukkan bahwa media terbaik untuk induksi kalus
embriogenik adalah MS yang diperkaya TDZ 0,1 mg l-1 yang
menghasilkan kalus embriogenik dengan struktur agak remah.
Kasein hidrolisat dan ekstrak malt tidak berpengaruh nyata
dalam menginduksi pembentukan embrio somatik manggis.
Setelah dua kali subkultur pada media yang sama, yaitu MS
yang diperkaya TDZ 0,5 mg l-1 dan BA 0,7 mg l-1, dihasilkan
33,8 embrio per eksplan. Keberhasilan embrio-genesis somatik
ini akan mendukung program pemuliaan tanaman dan
perbanyakan benih massal manggis secara in vitro.
(Penulis)
Kata kunci: Garcinia mangostana, zat pengatur tumbuh,
induksi kalus, embrio somatik
————————————————————————UDC: 635.356-152
Nur Kholilatul Izzaha, Reflinurb dan Tae-Jin Yangc (aBalai
Penelitian Tanaman Industri dan Penyegar, Pakuwon,
Sukabumi, bBalai Besar Penelitian dan Pengembangan
Bioteknologi dan Sumberdaya Genetik Pertanian, BogorcDepartemen Ilmu Tanaman dan Balai Penelitian Pertanian
dan Biologi, Universitas Nasional Seoul, Seoul)
Pengembangan Marka EST-SSR untuk Analisis Keragaman
Genetik Tanaman Brokoli dan Kerabatnya (Orig. Eng.)
IJAS, April 2016, vol. 17 no. 1, p. 17–26, 5 tab., 4 ill., 31 ref.
Pengembangan marka Expressed Sequence Tag-Simple Sequence
Repeat (EST-SSR) yang berasal dari database publik dikenal
lebih efisien, cepat, dan berbiaya rendah. Tujuan penelitian ini
adalah untuk mendapatkan satu set marka EST-SSR baru untuk
brokoli dan kerabatnya, serta kegunaannya untuk analisis
keragaman genetik. Sebanyak 202 sekuen EST dari Brassica
oleracea yang diperoleh dari NCBI digunakan dalam penelitian
ini, yang selanjutnya dikelompokkan menjadi 172 unigenes
dengan menggunakan program CAP3. Identifikasi motif SSR
dilakukan menggunakan program RepeatMasker, sedangkan
marka EST-SSR didesain menggunakan program Primer3.
Sebanyak 12 SSR berhasil dideteksi dan di antara SSR yang
teridentifikasi, trinukleotida merupakan jenis pengulangan
yang paling banyak ditemukan, yaitu sekitar 50%. Selain itu,
delapan pasang primer berhasil didesain dan menghasilkan
produk amplifikasi. Hasil amplifikasi menunjukkan lima
primer bersifat polimorfis dan menghasilkan 30 alel dengan
rata-rata enam alel per lokus. Marka polimorfis tersebut
kemudian digunakan untuk menganalisis keragaman genetik 36
kultivar B. oleracea, yang meliputi 22 brokoli, 5 kol bunga,
dan 9 kohlrabi berdasarkan matriks kemiripan genetik seperti
yang diterapkan dalam program NTSYS. Pada koefisien
kesamaan 61%, UPGMA dendrogram berhasil mengelompok-
kan 36 genotipe menjadi tiga kelompok utama. Sebanyak 30
dari 36 genotipe tersebut berhasil dibedakan satu dengan yang
lainnya. Hasil yang diperoleh dalam penelitian ini dapat
membantu para pemulia dalam memilih tetua yang digunakan
untuk persilangan. Selain itu, marka EST-SSR yang didesain
pada penelitian ini merupakan suatu alat yang berharga untuk
membedakan kultivar-kultivar brokoli dan kerabatnya.
(Penulis)
Kata kunci: Brokoli, kol bunga, kohlrabi, Marka EST-SSR,
keragaman genetik
————————————————————————UDC: 634.773+635.965.274
Riry Prihatinia dan Norihan Mohamad Salehb (aBalai Penelitian
Buah Tropika, Solok, bDepartment Sel dan Biologi Molekuler,
Fakultas Bioteknologi dan Ilmu Biomolekuler, Universiti Putra
Malaysia 43400 UPM Serdang Selangor DEE)
Sensitivitas Kandungan Pigmen pada Kultur Jaringan Tanaman
Pisang dan Anggrek yang Terpapar Medan Elektromagnetik
Frekuensi Sangat Rendah (Orig. Eng.)
IJAS, April 2016, vol. 17 no. 1, p. 27–34, 1 tab, 2 ill., 38 ref.
Paparan alami medan elektromagnetik frekuensi sangat rendah
(ME-FSR) terdapat di lingkungan dan merupakan salah satu
faktor abiotik yang memengaruhi pertumbuhan dan perkem-
bangan makhluk hidup. Penelitian bertujuan untuk mengetahui
pengaruh paparan ME-FSR pada kandungan pigmen kultur
jaringan pisang dan anggrek sliper sebagai indikasi kapasitas
fotosintesis. Kultur pisang (Musa sp. cv. Berangan) dan
anggrek sliper (Paphiopedilum rothschildianum) dipapar
dengan ME-FSR 6 dan 12 mT selama 0,5; 1, 2, dan 4 jam.
Hasil penelitian menunjukkan bahwa paparan ME-FSR ber-
pengaruh berbeda terhadap kultur jaringan pisang dan anggrek
sliper, meskipun keduanya termasuk ke dalam monokotiledon.
Kandungan klorofil dan karoten/xantofil pada pisang yang
terpapar ME-FSR meningkat seiring dengan peningkatan
intensitas dan durasi paparan ME-FSR. Sebaliknya, kandungan
klorofil dan karoten/xantofil pada anggrek sliper berkurang
seiring dengan peningkatan intensitas dan durasi paparan ME-
FSR. Perbedaan paparan ME-FSR (12 mT selama 4 jam dan
16 mT selama 30 menit) berpeluang untuk diaplikasikan pada
kedua tanaman tersebut untuk meningkatkan pertumbuhan
tanaman. Penemuan ini mengindikasikan bahwa eksplan
pisang lebih toleran terhadap paparan MF-FSR dibandingkan
dengan anggrek sliper.
(Penulis)
Kata kunci: Pisang, anggrek, klorofil, karoten, medan
elektromagnetik
————————————————————————UDC: 633.683
Imron Riyadi dan Sumaryono (Balai Penelitian Bioteknologi
dan Bioindustri, Bogor)
Pengaruh Iradiasi Sinar Gamma terhadap Pertumbuhan dan
Perkembangan Kalus Tanaman Sagu (Metroxylon sagu Rottb.)
(Orig. Eng.)
IJAS, April 2016, vol. 17 no. 1, p. 35–40, 2 tab., 3 ill., 22 ref.
Aplikasi iradiasi sinar gamma pada bahan tanaman dapat
meningkatkan keragaman genetik pada keturunan baru dengan
sifat-sifat unggul yang bermanfaat. Percobaan ini bertujuan
untuk menentukan pengaruh dosis iradiasi sinar gamma pada
pertumbuhan dan perkembangan kalus sagu (Metroxyon sagu).
Kalus remah sagu yang berasal dari kultur suspensi digunakan
sebagai sumber bahan penelitian. Kalus primer tersebut berasal
dan hasil induksi jaringan meristem pucuk dari anakan sagu
varietas Alitir yang berasal dari Merauke, Papua. Perlakuan
yang diuji adalah dosis iradiasi sinar gamma yang terdiri atas 0,
5, 10, 15, 20, dan 25 Gy. Kalus yang telah diberi perlakuan
iradiasi sinar gamma kemudian disubkultur pada media padat
Murashige dan Skoog yang dimodifikasi (MMS) mengandung
3% sukrosa dan 0,1% arang aktif, serta zat pengatur tumbuh
2,4-D 1 mg l -1 dan kinetin 0,1 mg l -1. Hasil penelitian
menunjukkan bahwa semua perlakuan dosis iradiasi sinar
gamma dapat meningkatkan biomassa kalus secara nyata.
Penggandaan biomassa kalus tertinggi sebesar 5,33 kali lipat
dari awal kultur setelah empat minggu dicapai pada perlakuan
dosis sinar gamma 25 Gy, sedangkan penggandaan biomassa
kalus terendah sebesar 3,4 kali lipat diperoleh pada kontrol.
Perkembangan kalus embriogenik terbaik dicapai pada
perlakuan 10 Gy yang mampu menghasilkan embrio somatik
100%, sedangkan pembentukan embrio somatik terendah
diperoleh pada kontrol dan 25 Gy setelah disubkultur satu kali.
Respons yang tinggi dari induksi embrio somatik terhadap
sinar gamma pada dosis 10 Gy meningkatkan produksi embrio
somatik. Hasil yang diperoleh dapat digunakan dalam
pemuliaan in vitro tanaman sagu melalui mutagenesis untuk
menghasilkan varietas unggul baru.
(Penulis)
Kata kunci: Metroxylon sagu, iradiasi sinar gamma, kalus
embriogenik, embrio somatik
————————————————————————UDC: 634.441.2-167
Nani Heryani, Budi Kartiwa, Yayan Apriyana dan Haris
Syahbuddin (Balai Penelitian Agroklimat dan Hidrologi, Bogor)
Peningkatan Produksi dan Kualitas Mangga Melalui Teknik
Irigasi Curah (Orig. Eng.)
IJAS, October 2016, vol. 17 no. 2, p. 41–48, 6 tab., 4 ill., 36 ref.
Kekurangan air pada fase reproduksi (pembungaan, pembentuk-
an buah, dan pematangan) dapat menurunkan produksi dan
kualitas mangga. Dengan demikian pada fase-fase tersebut
tanaman harus terhindar dari cekaman air. Tujuan penelitian
adalah mengukur pengaruh pemberian irigasi terhadap hasil dan
kualitas buah mangga. Penelitian dilaksanakan di Kebun
Percobaan Cukurgondang, Pasuruan, Jawa Timur, pada April–
Desember 2013 menggunakan 40 pohon mangga varietas
Arum Manis umur 21 tahun, dengan jarak tanam 6 m x 6 m.
Teknik irigasi curah (fan jet sprayer) menggunakan selang
dipasang sesuai diameter pohon dengan empat buah nozzle per
pohon. Lima perlakuan irigasi yang diaplikasikan yaitu 125,
100, 75, 50, dan 0% dari kebutuhan air tanaman atau berturut-
turut setara dengan 828, 663, 497, 331, dan 0 liter air per
tujuh hari per pohon. Parameter yang diamati yaitu jumlah dan
berat buah rontok, jumlah dan berat buah yang dipanen, serta
kualitas buah. Hasil penelitian menunjukkan bahwa perlakuan
irigasi 50% dan 75% dari kebutuhan tanaman masing-masing
menghasilkan jumlah buah rontok terbanyak dan terendah,
yaitu berturut-turut 26% dan 14% dari total produksi. Jumlah
buah total tertinggi dan terendah masing-masing terdapat pada
perlakuan irigasi 50% dan 75% dari kebutuhan air tanaman,
berturut-turut 3.108 dan 1.904 buah. Total berat buah tertinggi
dan terendah terdapat pada perlakuan irigasi 50% dan 125%
dari kebutuhan air tanaman, yaitu berturut-turut 1036,2 dan
677,9 kg. Berat buah mangga yang dihasilkan umumnya
termasuk kelas 2 dan 3 dengan kualitas A.
(Penulis)
Kata kunci: Mangga, produksi, kualitas, irigasi curah
————————————————————————UDC: 633.15-152
Edy Listanto, Eny Ida Riyanti dan Sustiprijatno (Balai Besar
Penelitian dan Pengembangan Bioteknologi dan Sumberdaya
Genetik Pertanian, Bogor)
Transformasi Tanaman Jagung Indonesia dengan Plasmid
pIG121Hm-Cs yang Mengandung Gen nptII dan hpt melalui
Agrobacterium tumefaciens secara In-Planta (Orig. Eng.)
IJAS October 2016, vol. 17 no. 2, p. 49–56, 1 tab., 5 ill., 33 ref.
Upaya peningkatan produktivitas jagung dapat dilakukan
melalui rekayasa genetik tanaman. Proses transformasi
merupakan kunci keberhasilan dalam rekayasa genetik
tanaman. Metode transformasi in-planta menggunakan
Agrobacterium tumefaciens merupakan metode transformasi
yang sederhana dan murah. Penelitian ini bertujuan melakukan
konfirmasi konstruksi gen pada plasmid pIG121Hm-Cs di
dalam A. tumefaciens, dan menduga tingkat efisiensi
transformasi melalui Agrobacterium secara in planta pada
tanaman jagung Indonesia dengan plasmid pIG121Hm-Cs yang
mengandung gen nptII dan hpt. Penelitian dilaksanakan
melalui beberapa tahapan secara berurutan, yaitu konfirmasi
konstruksi gen pada plasmid pIG121Hm-Cs dalam A.
tumefaciens, transformasi empat galur jagung melalui A.
tumefaciens dengan teknik in-planta, aklimatisasi tanaman
transforman, dan analisis molekuler tanaman transforman
terseleksi menggunakan polymerase chain reaction (PCR).
Keberadaan plasmid pIG121Hm-Cs dikonfirmasi dengan
analisis PCR menggunakan primer spesifik untuk gen nptII dan
hpt dan dihasilkan fragmen DNA berukuran 700 pb untuk gen
nptII dan 500 pb untuk gen hpt. Setelah tahap seleksi,
aklimatisasi, dan analisis molekuler, efisiensi transformasi
keempat galur jagung masih rendah, berkisar antara 3,8–
12,8%. Tingkat efisiensi transformasi tertinggi ditunjukkan
oleh galur jagung ST-27, yaitu 12,8% dari 45 embrio yang
ditanam pada media seleksi berdasarkan analisis PCR
menggunakan primer spesifik untuk gen nptII. Berdasarkan
hasil tersebut, transformasi tanaman jagung melalui A.
tumefaciens secara in-planta pada putik bunga terbukti berhasil
dan cepat. Metode transformasi ini akan bermanfaat untuk
rekayasa genetik pada tanaman jagung.
(Penulis)
Kata kunci: Jagung, Agrobacterium tumefaciens, transformasi
in-planta
————————————————————————UDC: 633.74-152
I Made Tasmaa, Dani Satyawana, Habib Rijzaania, Ida
Rosdiantia, Puji Lestaria dan Rubiyob (aBalai Besar Penelitian
dan Pengembangan Bioteknologi dan Sumberdaya Genetik
Pertanian, Bogor, bBalai Penelitian Tanaman Industri dan
Penyegar, Pakuwon)
Variasi Genom Lima Varietas Kakao (Theobroma cacao L.)
Indonesia Berdasarkan Analisis Menggunakan Next Generation
Sequencing (Orig. Eng.)
IJAS October 2016, vol. 17 no. 2, p. 57–64, 3 tab., 2 ill., 42 ref.
Produktivitas kakao Indonesia masih rendah antara lain
karena kurang tersedianya bahan tanaman unggul. Metode
pemuliaan baru perlu diterapkan untuk mempercepat program
pemuliaan kakao nasional. Sampai saat ini belum ada
penelitian untuk mengkarakterisasi varietas kakao Indonesia
pada level genom total. Penelitian ini bertujuan untuk
mengidentifikasi variasi genom varietas unggul kakao
Indonesia menggunakan next generation sequencing. Materi
genetik yang digunakan adalah lima varietas unggul kakao
Indonesia, yaitu ICCRI2, ICCRI3, ICCRI4, SUL2, dan ICS13.
Data sekuen genom kelima varietas tersebut dijajarkan dengan
sekuen genom rujukan kakao varietas Criollo. Penjajaran
sekuen dilakukan menggunakan software Bowtie2 dan
identifikasi variasi genom (SNP dan Indel) dilakukan dengan
software mpileup dari Samtools. Penelitian ini meng-hasilkan
variasi genom sebanyak 2.688.169 yang terdiri atas 2.326.088
SNP dan 362.081 insersi dan delesi (Indel). Secara rata-rata
satu variasi genom (SNP atau Indel) ditemukan pada setiap 121
basa dari sekuen genom kakao. Dari seluruh SNP yang
diidentifikasi, 347.907 SNP (13,18%) berlokasi pada protein
coding region. Dari jumlah ini, 188.949 SNP menyebabkan
mutasi yang mengubah susunan asam amino pada protein
(missense mutation) dan 1.535 SNP menyebabkan mutasi yang
menghasilkan stop codon (nonsense mutation). Ditemukan
juga SNP berbasis gen yang unik pada setiap genotipe kakao
yang dapat digunakan sebagai sidik jari dari setiap genotipe
kakao yang diuji. Variasi genom yang dihasilkan merupakan
sumber daya marka DNA bernilai tinggi untuk studi genetika
dan pemuliaan kakao. SNP hasil penelitian ini dapat digunakan
sebagai materi untuk pembuatan SNP chip kapasitas tinggi yang
bermanfaat untuk pelabelan gen unggul dan QTL yang terkait
karakter penting untuk mendukung percepatan program
pemuliaan kakao nasional.
(Penulis)
Kata kunci: Theobroma cacao, sekuensing genom total, variasi
genom, SNP, next generation sequencing
————————————————————————UDC: 633.3-152
Reflinura, Puji Lestaria dan Suk-Ha-Leeb (aBalai Besar
Penelitian dan Pengembangan Bioteknologi dan Sumberdaya
Genetik Pertanian, Bogor, bDepartemen Ilmu Tanaman dan
Balai Penelitian Pertanian dan Biologi, Universitas Nasional
Seoul)
Potensi Penggunaan Marka SSR dalam Mendukung Identifikasi
Morfologi Varietas Kacang Hijau Indonesia (Orig. Eng.)
IJAS, October 2016, vol. 17 no. 2, p. 65–74, 4 tab., 2 ill., 31 ref.
Karakterisasi kacang hijau pada umumnya dilakukan
berdasarkan sifat-sifat morfologi. Pendekatan genetika
molekuler diharapkan dapat membantu pemulia dalam
mengidentifikasi kacang hijau dan melindungi hak kekayaan
intelektual pemulia. Penelitian ini bertujuan untuk
mengidentifikasi varietas kacang hijau Indonesia berdasarkan
penampilan sidik jari DNA dengan menggunakan satu set
marka untuk mendukung karakterisasi secara morfologi.
Sebanyak 22 aksesi kacang hijau Indonesia telah dianalisis
berdasarkan 21 karakter morfologi dan secara molekuler
menggunakan 55 primer simple sequence repeats (SSR). Di
antara 22 varietas kacang yang digunakan pada penelitian ini,
16 varietas merupakan varietas unggul dan enam varietas
merupakan varietas lokal asal Jawa, Nusa Tenggara, dan
Sulawesi yang dikoleksi di BankGen BB Biogen. Hasil
penelitian menunjukkan bahwa 21 karakter morfologi yang
digunakan belum cukup informatif untuk membedakan 22
varietas kacang hijau. Berdasarkan analisis SSR, delapan marka
dan nilai informasi polimorfis yang tinggi telah terseleksi
sebagai marka untuk identifikasi varietas kacang hijau. Set
marka terseleksi tersebut mampu membedakan masing-masing
varietas dengan jarak genetik terendah sebesar 0,125 dan
secara spesifik dapat digunakan sebagai alat bantu yang andal
untuk identitas varietas (ID). Identitas genetik dari varietas
tersebut ditunjukkan oleh angka barcoding yang merupakan
rentetan dari alel-alel yang dihasilkan oleh masing-masing
marka. Profil sidik jari DNA dari masing-masing varietas
kacang hijau akan sangat bermanfaat terutama sebagai referensi
identitas varietas kacang hijau.
(Penulis)
Kata kunci: Kacang hijau, karakter morfologi, SSR, sidik jari
DNA, identitas varietas
UDC: 631.445.1
Muhammad Imam Nugrahaa, Wahida Annisab, Lailan Syaufinac
dan Syaiful Anward, aMahasiswa Pascasarjana di Institut
Pertanian Bogor, bBalai Penelitian Pertanian Lahan Rawa,
Banjarbaru, cFakultas Kehutanan, Institut Pertanian Bogor,dFakultas Pertanian, Institut Pertanian Bogor)
Kenaikan Air Kapiler di Tanah Gambut Akibat Pengaruh
Berbagai Ketinggian Muka Air Tanah (Orig. Eng.)
IJAS, October 2016, vol. 17 no. 2, p. 75–83, 3 tab., 6 ill., 31 ref.
Air kapiler di lahan gambut memiliki peranan yang sangat
penting dalam menyediakan air untuk zona perakaran
tanaman. Kadar air tanah aktual pada zona perakaran sangat
bergantung pada tinggi muka air tanah pada suatu kawasan
yang mempunyai tinggi muka air yang dangkal. Tujuan
penelitian adalah untuk mengukur dinamika kapilaritas tanah
gambut pada berbagai faktor kepadatan tanah dan tinggi muka
air tanah yang diamati dari perubahan warna, distribusi
kelembapan, kadar air, dan hidrofobisitas tanah gambut.
Penelitian dilaksanakan di rumah kawat Balai Penelitian
Pertanian Lahan Rawa, Banjarbaru, Kalimantan Selatan.
Penelitian menggunakan rancangan acak kelompok faktorial
dengan dua faktor yang diulang tiga kali. Faktor pertama
adalah tingkat kepadatan gambut (BD), yaitu BD-1 (kondisi
aktual, 0,1 g cm-3) dan BD-2 (dipadatkan menjadi 0,2 g cm-3).
Faktor kedua adalah simulasi tinggi muka air tanah (GWL)
berdasarkan tinggi pipa mika, yaitu GWL-1 (-100 cm), GWL-
2 (-70 cm), dan GWL-3 (-40 cm). Hasil penelitian menunjuk-
kan tinggi kenaikan air kapiler di tanah gambut maksimum
mencapai 50 cm yang dicirikan dengan meningkatnya nilai
kelembapan tanah antara 105–127% pada BD-1 dan 141–
181% pada BD-2. Nilai kadar air tanah tertinggi terlihat pada
perlakuan GWL-3 dengan BD-2 sebesar 308% dan yang
terendah pada perlakuan GWL-1 dengan BD-1 sebesar 37%.
Kecepatan kenaikan air kapiler semakin tinggi dengan
meningkatnya nilai BD tanah karena terkait dengan jumlah
pori mikro yang lebih banyak pada BD-2.
(Penulis)
Kata kunci: Tanah gambut, air kapiler, tinggi muka air tanah,
kepadatan gambut, kelembapan tanah
INTRODUCTION
Mungbean (Vigna radiata L. (Wilczek)), a second
economically important legume crop in Indonesia
after soybean, is an important source of protein,
vitamin and mineral (Tomooka et al. 2002; Lambrides
and Godwin 2007; Somta and Srinives 2007; Mondalet al. 2012). In spite of the best efforts for improving
mungbean varieties, the yield of this crop remains
low. According to the Central Bureau Statistics of
Indonesia, the national mungbean productivity was
1.12 ton ha"1 with the total area of 182,058 ha (BPS
2013). Therefore, the genetic improvement of mung-
satu set marka untuk mendukung karakterisasi secara morfologi.Sebanyak 22 aksesi kacang hijau Indonesia telah dianalisisberdasarkan 21 karakter morfologi dan secara molekulermenggunakan 55 primer simple sequence repeats (SSR). Di antara22 varietas kacang yang digunakan pada penelitian ini, 16 varietasmerupakan varietas unggul dan enam varietas merupakan varietaslokal asal Jawa, Nusa Tenggara, dan Sulawesi yang dikoleksi diBankGen BB Biogen. Hasil penelitian menunjukkan bahwa 21karakter morfologi yang digunakan belum cukup informatif untukmembedakan 22 varietas kacang hijau. Berdasarkan analisis SSR,delapan marka dan nilai informasi polimorfis yang tinggi telahterseleksi sebagai marka untuk identifikasi varietas kacang hijau.Set marka terseleksi tersebut mampu membedakan masing-masingvarietas dengan jarak genetik terendah sebesar 0,125 dan secaraspesifik dapat digunakan sebagai alat bantu yang andal untukidentitas varietas (ID). Identitas genetik dari varietas tersebutditunjukkan oleh angka barcoding yang merupakan rentetan darialel-alel yang dihasilkan oleh masing-masing marka. Projil sidikjari DNA dari masing-masing varietas kacang hijau akan sangatbermanfaat terutama sebagai referensi identitas varietas kacanghijau.
[Kata kunci: Kacang hijau, karakter morfologi, SSR, sidik jari DNA,identitas varietas]
ABSTRAK
Karakterisasi kacang hijau pada umumnya dilakukan berdasarkansifat-sifat morfologi. Pendekatan genetika molekuler diharapkandapat membantu pemulia dalam mengidentifikasi kacang hijaudan melindungi hak kekayaan intelektual pemulia. Penelitian inibertujuan untuk mengidentifikasi varietas kacang hijau Indonesiaberdasarkan penampilan sidik jari DNA dengan menggunakan
ABSTRACT
Mungbean varieties were mainly characterized based onmorphological traits. Molecular genetic approach is expectedto help the breeder in identification of mungbean varieties inmore detail and to protect intellectual property right. Thisstudy aimed to identify Indonesian mungbean varieties based onDNA fingerprint profile using a marker set to supportmorphological characters. A total of 22 Indonesian mungbeanaccessions were characterized based on 21 morphological traitsand 55 simple sequence repeats (SSRs) primers. Of the total 22mungbean varieties used in the present study, 16 varieties wereimproved varieties and remaining six varieties were localvarieties originated from Java, Nusa Tenggara and Sulawesicollected in GeneBank of ICABIOGRAD. The results showedthat the 21 morphological characters were not sufficient todifferentiate 22 mungbean varieties, while SSR analysisrevealed that eight multi-alleles markers and high polymorphicinformation content (PIC) values have been successfully selectedfor varietal identification. The selected markers enabled todifferentiate each mungbean variety according to their geneticmarker with the lowest distance of 0.125, demonstrating therobustness of the selected marker set as a tool to identify aspecific DNA fingerprint profile as a varietal identity (ID). Thegenetic identity of a variety was shown by digital barcodingwhich represented a series of alleles produced by correspondingmarkers. The DNA fingerprint profile of each variety would bebeneficial as reference identities of a mungbean variety.
[Keywords: Mungbean, morphological characters, SSR markers,DNA fingerprint, varietal identity]
THE POTENTIAL USE OF SSR MARKERS TO SUPPORT THE MORPHOLOGICALIDENTIFICATION OF INDONESIAN MUNGBEAN VARIETIES
Potensi Penggunaan Marka SSR dalam Mendukung Identifikasi MorfologiVarietas Kacang Hijau Indonesia
Reflinur3, Puji Lestari" and Suk-Ha Leeb
"Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and DevelopmentJalan Tentara Pelajar No. 3A, Bogor 16111, West Java, Indonesia
Phone +62 251 8337975, Fax. +62 251 8338820bDepartment of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University
Corresponding author: [email protected]
Submitted 16 March 2016; Revised 13 September 2016; Accepted 20 September 2016
DOI: http//dx.doi.org/10.21082/ijas.vl7n2.2016.p65-74Indonesian Journal of Agricultural ScienceVol. 17 No. 2 October 2016: 65-74
MATERIALS AND METHODS
Plant Materials
A total of 22 Indonesian mungbean varieties consisted
of 16 improved varieties and six local varieties as a
comparison were subjected to both morphological
and molecular analyses (Table 1). All of the accessions
belonged to the genebank of the Indonesian Center
for Biotechnology and Genetic Resources Research
and Development (ICABIOGRAD), Bogor, West Java.
previously. In this study, a total of 30 newly SSR
simple sequence repeat (SSR) markers which were
developed from the genome of Korean mungbean
varieties (Sunhwanokdu and Gyeonggijaerae 5)
proved their application to detect genetic variability
of 83 accessions of Indonesian mungbean to support
breeding program and conservation strategy.
Moreover, these markers were able to identify
improved mungbean varieties that were genetically
similar to some landraces from one of the main
mungbean-producing regions in Indonesia (Lestari et
al. 2014). Considering the prospecting SSR markers
(Lestari et al. 2014), our current study applied those
markers in addition to other markers for varietal
identification rather than genetic diversity study. The
use of molecular markers which discriminate varieties
in nucleotide sequences are unaffected by
environments and becomes more desirable in varietal
identification and differentiation.
SSR markers have been the most widely-used
genotyping markers in many plant species over the
past decade due to their stability, ease of application,
representing highly polymorphic, abundant presence
in the genome, reproducible, co-dominant, and
multiallelic types of variation (Minamiyama et al.
2006; Yi et al. 2006; Lorenzo et al. 2007; Portis et al.
2007; Agarwal et al. 2008; Senthilvel et al. 2008;Sundaram et al. 2008; Kumar et al. 2009). The working
group on biochemical and molecular techniques of
UPOV has identified SSR markers as the predominant
markers for plant varietal characterization (UPOV
2011). A specific set of SSRs can be used indifferentsets of genotypes, making them particularly useful for
DNA fingerprinting.
The objective of this study was to identifyIndonesian mungbean varieties based on DNA
fingerprint profile using a set of developed markers to
support the morphological characters.
bean should be based on the genetic information of
the plant.
Conservation of the genetic resources of mungbean
is vital for future breeding programs and food
security, therefore, characterization and proper
assignation of individual genotypes to species is
required (Karp 1996; Vincent et al. 2013). TheInternational Union for the Protection of New
Varieties of Plants (UPOV) has provided guidelines onestablishing the uniqueness of a variety through
testing for distinctiveness, uniformity and stability
(DUS) (UPOV 2011). Through the adoption of theUPOV system, a breeder is obliged to protect a
variety for commercial exploitation. Protection can be
granted if a variety of the crop is distinct from the
existing ones supported with sufficiently uniform and
stable genetic characteristics. Hence, the varietal
identification of mungbean becomes a critical
importance.Traditionally, the accessions of mungbean in
Indonesia are characterized based on their
morphological and physiological traits (Van den
Bosch 1987; Hakim 2008). Van den Bosch (1987)reported an intercropping of mungbean landraces
originated from East Java with maize. After three
cycles of selection, a yield of intercropped mungbean
increased 24% as compared to the original mungbean
landraces, and the yield of maize in the mixture was
not affected by the increase in mungbean landrace
yield. In another study, Hakim (2008) evaluated 350
mungbean accessions for their agronomic characters
in the field. A number of these characters (days to
maturity, plant height, pods per plant and seed size)
were known to be significantly varied. Number of
pods per plant and plant height were important
characters that can be used as the selection criteria in
mungbean breeding in the early generation stage
(Hakim 2008). However, this traditional method is
costly and time-consuming since numbers of existing
varieties are quite large that require wide land and
skilled personnel, and often subjective decisions
(Cooke 1995; Kumar et al. 2009). Therefore, reliable
and cost-effective methods for identifying varieties
are desirable to differentiate the increasing numbers
of new varieties and eliminate duplicates from
germplasm collections. An effective method for
variety identification such as DNA fingerprinting is
essential for DUS testing of new varieties and for
protection of intellectual property right of new
varieties (Lu et al. 2009).
The use of molecular markers for differentiating
mungbean varieties of Indonesia has been reported
Indonesian Journal of Agricultural Science Vol. 17 No. 2 October 2016: 65-7466
PCR Amplification
PCR reactions were conducted in a total volume of 20
pi and contained 20 ng genomic DNA, 0.25 pM each
primer (forward and reverse), 0.125 mM each dNTP,
0.16 units AmpliTaq Gold® DNA Polymerase (AppliedBiosystem, Warrington, UK), and lx AmpliTaq buffer
with MgCl2. The PCR amplification was performed
using a 96-well plate in a tetrad thermal cycler (DNA
Engine Tetrad, MJ Research). The amplification
conditions were as recommended by the manu
facturer's protocol (Applied Biosystem, Warrington,
UK) that consisted of an initial denaturation step of 5
minutes at 94 C, followed by 35 cycles of 45 seconds
at 94 C, 30 seconds at 55 C, 30 seconds at 72 C
with a final extension at 72 C for 10 minutes. PCR
products were first separated on 2% (w/v) agarose
(Gelvin and Schilperoort 1995). For an initialscreening, a total of 55 SSR markers developed in the
Crop Genomic Laboratory, Seoul National University
were used on the basis of de novo sequencing data
of Korean mungbean cultivars (Sunhwanokdu and
Gyeonggijaere). Then the DNA polymorphisms of 22Indonesian mungbean varieties were checked by a
fluorescence-based capillary electrophoresis.
DNA Isolation
Young and healthy leaves of three to four day-old
mungbean seedlings were harvested for DNA
extraction. The leaf tissues were ground into a fine
powder in a liquid nitrogen by a pestle and mortar.
The genomic DNA was extracted using a standard
cetyltrimethylammonium bromide (CTAB) method
Morphological Characterization
All genetic materials were grown at the Experimental
Farm of Seoul National University in Suwon, Korea
(altitude: 74 m, longitude: 127362 E, latitude: 37512 N)following the standard cultural practices. Two
individual plants were grown in each pot with two
replications. Twenty one qualitative morphological
characters related to growth habit, leaf, stem and pod
were observed and scored according to the guidelines
for conducting tests for distinctness, homogeneity and
stability criteria provided by the UPOV (UPOV 2011).All recorded characters were converted to numerical
numbers which could be designed as digital morpho
logical markers of each mungbean variety. Based on
the qualitative morphological data, a phylogenetic tree
was generated using PowerMarker software.
Si WalikSelected from a population in JenepontoArta IjoSelected from local varieties originating from Sumenep, MaduraManyarIntroduced varieties from AVRDC (Taiwan)BhaktiSelected from introduced varieties from Sri LankaNo. 129Selected from introduced varieties from PhilippinesNuriSelected from introduced varieties from AVRDC (Taiwan)KenariIntroduced from AVRDC, Taiwan 1987, single cross from VC 1178B as
male and VC 1624 as femaleBetetSelected from cross of MB 129 x SiwalikGelatikSelected from introduced varieties from AVRDC (Taiwan)ParkitPHLV-18/VC.1177 1979MerpatiSelcted from F4 generation of introduced lines from TaiwanWaletSelected from introduced varieties from AVRDC (Taiwan)CamarDeveloped using Gamma irradiation of 0.1 kGy dose on Manyar varietyMerakSelected from introduced varieties from PhilippinesPerkututIntroduced from AVRDC, TaiwanVima-1Synthetic crossing of VC 1973 A and 2750ANilonSulawesiLok BeluNusa TenggaraLok GarutJavaTecer HijauJavaLok NTBNusa TenggaraLok Muntaha K2 Sulawesi
Genetic background/originVariety
Table 1. Twenty two Indonesian mungbean varieties used in this study together withtheir origin or genetic background.
67The potential use of SSR markers to support the morphological ... (Reflinur, Puji Lestari and Suk-Ha Lee)
RESULTS AND DISCUSSION
Variability of Mungbean Varieties Based onMorphological Characters
Twenty one qualitative morphological characters of
22 Indonesian mungbean varieties were presented on
Table 2. The present data indicated that a low
variation (0.28) was evidenced in all mungbean
varieties evaluated. Seven morphological characters
were uniform, whereas the remaining ones were
considerably varied ranging from low (0.04) for
mature pod color to the highest (0.81) for leaf
pubescence character. A moderate degree of variation
was observed in the leaf color, stem color and seed
size. All varieties showed no lobe of leaf, ovate
lanceolate shape of primary leaf, deltate of terminal
leaf, drum of seed, yellow flower, pod pubescence
and green color of premature pod. Majority (> 80%)
of varieties had seed pubescence, straight of pod
curvature and green seed. According to mature pod
characteristics, only a local variety of Tecer Hijau
from Java had a brown color in contrast the green
one of the rest varieties.
The morphological character data showed common
on both improved and local varieties, and some traits
might be specific to genotypes as demonstrated in
our study. The morphological characters of released
varieties could be selected as important descriptor for
breeding program (Stoilova et al. 2013). While, local
varieties with better adaptation to local growing
regions possessed valuable character for cultivation
in different agroecological conditions (Stoilova and
Sabeva2006).To simply identify, the total of 21 characters were
scored and converted to numerical number (Table 1).
When morphological characters were used as
markers, it was noted that each genotype either
improved variety or local variety had its own identity.
However, these total morphological characters were
enabled to differentiate each mungbean variety yet.
As a representative, a variety named Parkit with
morphological identity of "221231211111213211211"and a variety named No. 129 with its code of
"121231211111213211211" seemed to be close anddiffered based on only one character, plant habit as
SSR motif observed on each primer. This digital code
transformation would be done for total SSR in the
formulated marker set and the digital codes
represented the ID of each mungbean variety
(Risliawati etal. 2015).
Data Analysis
Genotypic data were subjected to PowerMarker
software to analyze the polymorphic information
content (PIC) values of the tested primers, for the
calculation of allele number, allele frequency,
heterozygosity, gene diversity, and probability of
identity per locus. The PIC values of each SSR marker
were calculated for the total population (Liu 2001). SSRmarkers that exhibit high value of PIC (> 0.5) were
chosen to be recommended as valuable SSR markers
on DNA fingerprinting of Indonesian mungbean
varieties. Such information is important to be used as
basic criteria to select molecular markers candidate for
varietal identification. In parallel with selection of SSRs
for marker set, estimated calculation of genetic distance
through generating phylogenetic tree was performed
to maximize the varietal differentiation efficiency.
The polymorphic bands of 22 mungbean varieties
were scored as binary characters for their presence
(1) or absence (0) and the resulting data were
analyzed using NTSYS-PC (Numerical Taxonomy and
Multivariate Analysis System) version 2.1 (Rohlf
1998). Genetic similarity between cultivars was
calculated based on the simple matching coefficient
using the SIMQUAL subprogram. Cluster analysis
was performed using the Unweighted Pair Group with
Arithmetic Mean (UPGMA) method in the SAHNsubprogram of NTSYS-PC. This phylogenetic
analysis assisted to formulate SSR marker set to
identify mungbean variety.
The genetic identity (ID) of mungbean variety wasthen determined by a digital value which represented
a series of alleles produced by corresponding marker.
In this step, the allele size was transformed to two
digits of numerical number produced by each marker.
The two digital codes were started from "01" for each
gel containing GelRed (Biotium) in 0.5x TBE buffer.
The amplicons were visualized under UV light, and
the sizes were estimated relative to the 100 bp DNA
ladder.For further determination of polymorphism, the
amplicons were run in a fluorescence-based capillary
electrophoresis using Fragment Analyzer CE System
(Advanced Analytical Technologies, Inc., USA). To
ensure reproducibility of amplification products, the
analyses were repeated at least twice. Allele sizes
were determined for each SSR locus using fragment
analysis software which was automatically offered by
the capillary electrophoresis Fragment Analyzer CE
System.
Indonesian Journal of Agricultural Science Vol. 17 No. 2 October 2016: 65-7468
effective to discriminate among improved mungbean
varieties along with the local ones. This results is in
agreement and relevant with the previous report
showing that the genetic differentiation based on
morphological characters in the species level of Vigna
is less sufficient (Tantasawat et al. 2010).
denoted by "2" on variety Parkit and "1" on variety
No 129. While between Walet and Perkutut were not
distinct each other as reflected by the same identity
of "211241311111113211211". These results suggestedthat the numerical morphological characters which
reflect the differences in the mungbean organs are not
Abbreviations: PH = plant habit, GH = growth habit, StC = stem color, SP = stem pubescence, LP = leaf pubescence, LL = leaf lobe, LC= leaf color, LVC = leaf vein color, PLS = primary leaf shape, TLS = terminal leaf shape, SSh = seed shape, PCv = pod curvature, BP =branching pattern, FC = flower color, SS = seed size, PP = pod pubescence, PPC = premature pod color, MPC = mature pod color, SL = seedlusture, SC = seed color, H = hypocotyle
1.Plant habit: 1 = ID (indeterminate), 2 = D (determinate)2.Growth habit: 1 = SE (semierect), 2 = SHE (semierect-horizontal)3.Stem color: 1 = LG (light green), 2 = DG (dark green), 3 = GP (mixed green-purple)4.Stem pubescence: 1 = G (globrous/absent of hair), 2 = P (pubescence/present of hair)5.Leaf pubescence: 1 = VSP (very sparsely pubescence), 2 = SP (sparsely pubescence), 3 = MP (moderately pubescence), 4 = VMP (very
moderately pubescence)6.Leaf lobe: 1 = no lobe, 2 = having lobe7.Leaf color: 1 = LG (light green), 2 = G (green), 3 = DG (dark green)8.Leaf vein color: 1 = G (green), 2 = GP (greenish purple)9.Primary leaf shape: 1 = OL (ovate lanceolate)10.Terminal leaf shape: 1 = deltate11.Seed shape: 1 = D (drum)12.Pod curvature: 1 = S (straight), 2 = C (curvature)13.Branching pattern: 1 = all, 2 = central14.Flower color: 1 = yellow.15.Seed size: 1 = small, 2 = medium, 3 = big16.Pod pubescence: 1 = globrous, 2 = pubescence17.Premature pod color: 1 = green18.Mature pod color: 1 = black, 2 = brown19.Seed lusture: 1 = dull, 2 = shiny20.Seed color: 1 = green, 2 = black, 3 = green yellowish, 4 = yellow21.Hypocotyl color: 1 = green, 2 = purple
2122221111111211212222
1111111131111131111111
1222121222222112122211
2 12 I2 12 12 12 12222222222222222 -
2313133332323333233222
1111111111111111111111
211 2 2
112221211122
1 1I 2I 21 21 11 11 21 1
lllilililillii ;i ;11111
2 1 11 1 12 1 12 1 12 1 12 1 11 1 11 1 11 1 11 1 11 1 11 1 11 1 11 1 11 1 11 1 12 1 11 1 12 1 12 1 12 1 12 1 1
3223122321322223223233
2321 131 14443443334333343
1 2 31 2 2
212 3 11 2 1
12
1 21 2I 2I 2I 2i 2I 2I 2I 2I 2I 21 21 2I 2'. 2
1112 :2222111221112
1212122222212211212111
VR1069VR1057VR1079VR1077VR1005VR997
VR1074VR1058VR423VR224VR222VR220VR219VR218VR217VR196VR137VR129VR116VR110VR26VR9-1
Tecer HijauLok GarutLok NTBLok BeluLok Muntaha K.2NilonLima-1PerkututMerakCamarWaletMerpatiParkitGelatikBetetKenariNuriNo.129BhaktiManyarArta IjoSi Walik
PH GH StC SP LP LL LC LVC PLS TLS SSh PCv BP FC SS PP PPC MPC SL SC HReg.number
Variety
name
Table 2. Morphological characteristics of 22 mungbean varieties used in present study.
69The potential use of SSR markers to support the morphological ... (Reflinur, Fuji Lestari and Suk-Ha Lee)
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Both morphological and molecular data demon
strated the diversity level of the Indonesian mung
bean varieties. Aphylogenetic analysis was generated
to initial estimation of varieties differentiation, leading
to the identification of each variety as a distinctive
individual (Fig. 2). Therefore, a dendrogram of the 22
Indonesian mungbean varieties was performed using
the genetic similarity matrix generated by the Nei
1973 similarity coefficient based on alleles producedby eight SSR markers. Two main clades appeared to
group 10 varieties (clade I) and the remainingvarieties (clade II). Both clades contained improved
varieties together with three local varieties, in which
Lok Belu (Nusa Tenggara), Lok Garut (Java), Tecer
Hijau (Java) belonged to clade I, and Nilon (Sulawesi),Lok NTB (Nusa Tenggara) and Lok Muntaha K2(Sulawesi) into clade II. Importantly, each variety was
clearly distinct with each other without the same
genetic distance.Based on the allele size of DNA fingerprint profile
using a marker set containing eight SSR loci, finally a
barcoding in the form of digital ID of each mungbean
variety was successfully developed (Table 4). For
example an improved variety of Si Walik had ID"0401030804010503", while Nuri which was found tohave heterozygote alleles automatically had two IDs
depending on the harbored alleles, 0501040504020102and 0101020705030207. Notably, local varieties fromJava (LokGarut and Tecer Hijau) seemed to be
discrepancy according to their barcoding. Two
improved varieties (Walet and Perkutut) that were not
able to be differentiated based on morphological
characters, by using eight markers finally were
SSR Marker Set Development and SpecificIdentity of Mungbean Varieties
To design marker set to identify DNA fingerprintprofile of variety as genetic identity needs several
steps including selection of marker candidate, design
method for marker set and creation of varietal ID in
the digital barcode. In this study, based on PIC, gene
diversity and allele number of each marker, finally 14
SSR loci candidate were selected from a total of 55
primers surveyed. Out of the chosen 14 SSR primers,
further selection was done to obtain eight primers as
a basis in the marker set formulation. These markers
included those with high PIC values ranging from0.63 to 0.79, namely P33, P95, P57, P87, P27, P29, P36
and P17. This simple SSR analysis containing
minimized markers (eight) could be a suitable method
for routine identification of mungbean varieties,awhich is in good agreement with the previousjeport
(Prammanee et al. 2000).
Gene diversity of this mungbean collection was
relatively high, 0.68. Loci P87 which had the highestPIC value, showed the highest gene diversity (0.82),
suggesting a positive correlation between PIC and
gene diversity. Discrepancy of genetic diversity based
PIC demonstrated that the choice of markers and
varieties affected the variation of molecular markers
used. Markers with high PIC value and are informative
turned out to be a marker set for DNA fingerprinting
analysis for identification and differentiation of
particular varieties (Bredemeijer et al. 2002).
0.63
0.720.530.540.750.650.630.790.530.640.570.670.510.750.59
PIC
0.003
0.000.000.000.050.000.000.000.000.000.000.000.000.000.00
Heterozygosity
0.68
0.740.610.610.780.700.660.820.580.700.640.710.580.780.67
diversityGene
5.14
84565784434383
numberAllele
0.43
0.450.500.500.300.410.550.270.590.410.450.410.550.320.36
frequencyMajor allele
Means
P17P16P69P36P29P27P87P74P57P45P95P7P33P59
Marker
Table 3. Summary of statistics of 14 simple sequence repeat (SSR) markersobserved in 22 Indonesian mungbean varieties.
71The potential use of SSR markers to support the morphological ... (Reflinur, Puji Lestari and Suk-Ha Lee)
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Agarwal, M., N. Shrivastava and H. Padh. 2008. Advances inmolecular marker techniques and their applications in plantsciences. Plant Cell Rep. 27: 617-631.
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REFERENCES
financially supported by a grant from the Next-
Generation BioGreen 21 Program of the Rural
Development Administration, Republic of Korea.
ACKNOWLEDGEMENT
Authors highly thank to Dr. Yang Jae Kang and Dr.
Sue K. Kim, Crops Genomics Laboratory, Seoul
National University, Korea for their assistance during
conducting this research work. This research was
CONCLUSION
A total of 22 improved and local varieties of
Indonesian mungbean showed a common morpho
logical characteristic with a low variation (0.28).
Seven morphological characters, i.e. leaf lobe,
primary leaf shape, terminal leaf shape, seed shape,
flower color, pod pubescence and premature pod
color were uniform and found a considerable level of
variability ranging from low (0.04) for mature pod
color to the highest (0.81) for leaf pubescence
character. The use of the eight SSR markers proved
usefulness for differentiating the Indonesian
mungbean varieties. Eight of the SSR markers have
facilitated a specific DNA fingerprint profile andcould be used as the reference genetic identity for
identification of Indonesian mungbean varieties.
distinguished the two with genetic distance of 0.125.
Thus, this analysis proved that the eight SSR markers
enabled to create specific DNA fingerprint profile on
each of the Indonesian mungbean varieties. These
barcodes which possibly provided reference genetic
identity (ID) along with marker set in our study could
assist effective protection and management of
mungbean germplasm/collection in genebank and
market in Indonesia. Importantly, molecular ID could
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to protect local variety from claim of other countries
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Indonesian Journal of Agricultural Science Vol. 17 No. 2 October 2016: 65—7474
85
INDONESIAN JOURNAL OF AGRICULTURAL SCIENCE
Vol. 17, 2016: 1–83
Author Index
A
Annisa, Wahida, "Iron Dynamics and Its Relation to Soil Redox
Potential and Plant Growth in Acid Sulphate Soil of South
Kalimantan, Indonesia", 17(1): 1–8
Annisa,Wahida, "Capillary Water Rise in Peat Soil As Affected By
Various Groundwater Levels", 17(2): 75–83
Anwar, Syaiful, "Capillary Water Rise in Peat Soil As Affected By
Various Groundwater Levels", 17(2): 75–83
Apriyana,Yayan, "Production and Quality Enhancement of Mango
Using Fan Jet Sprayer Irrigation Technique", 17(2): 41–48
E
Efendi, Darda, "Effect of Different Sources of Plant Growth
Regulator on The Induction and Development of Mangosteen
Somatic Embryos", 17(1): 9–16
H
Heryani, Nani, "Production and Quality Enhancement of Mango
Using Fan Jet Sprayer Irrigation Technique", 17(2): 41–48
I
Izzah, Nur Kholilatul, "Development of EST-SSR Markers to Assess
Genetic Diversity of Broccoli and Its Related Species", 17(1): 17–26
K
Kartiwa, Budi, "Production and Quality Enhancement of Mango
Using Fan Jet Sprayer Irrigation Technique", 17(2): 41–48
L
Lestari, Puji, "Genomic Variation of Five Indonesian Cacao
(Theobroma cacao L.) Varieties Based on Analysis Using Next
Generation Sequencing", 17(2): 57–64
Lestari, Puji, "The Potential Use of SSR Markers to Support the
Morphological Identification of Indonesian Mungbean Varieties",
17(2): 65–74
Listanto, Edy, "Agrobacterium tumefaciens-Mediated In-Planta
Transformation of Indonesian Maize Using plG121Hm-Cs
Plasmid Containing nptII and hpt Genes", 17(2): 49–56
N
Nugraha, Muhammad Imam, "Capillary Water Rise in Peat Soil As
Affected By Various Groundwater Levels", 17(2): 75–83
Nursyamsi, Dedi, "Iron Dynamics and Its Relation to Soil Redox
Potential and Plant Growth in Acid Sulphate Soil of South
Kalimantan, Indonesia", 17(1): 1–8
J
Joni, Yosi Zendra, "Effect of Different Sources of Plant Growth
Regulator on The Induction and Development of Mangosteen
Somatic Embryos", 17(1): 9–16
Indonesian Journal of Agricultural Science/Author Index 85-1
P
Prihatini, Riry, "Effect of Different Sources of Plant Growth
Regulator on The Induction and Development of Mangosteen
Somatic Embryos", 17(1): 9–16
Prihatini, Riry, "Sensitivity of Pigment Content of Banana and Orchid
Tissue Culture Exposed to Extremely Low Frequency
Electromagnetic Field", 17(1): 27–34
R
Reflinur, "Development of EST-SSR Markers to Assess Genetic
Diversity of Broccoli and Its Related Species", 17(1): 17–26
Reflinur, "The Potential Use of SSR Markers to Support the
Morphological Identification of Indonesian Mungbean Varieties",
17(2): 65–74
Rijzaani, Habib, "Genomic Variation of Five Indonesian Cacao
(Theobroma cacao L.) Varieties Based on Analysis Using Next
Generation Sequencing", 17(2): 57–64
Riyadi, Imron, "Effect of Gamma Irradiation on The Growth and
Development of Sago Palm (Metroxylon sagu Rottb.) Calli",
17(1): 35–40
Riyanti, Eny Ida, "Agrobacterium tumefaciens-Mediated In-Planta
Transformation of Indonesian Maize Using plG121Hm-Cs
Plasmid Containing nptII and hpt Genes", 17(2): 49–56
Roostika, Ika, "Effect of Different Sources of Plant Growth
Regulator on The Induction and Development of Mangosteen
Somatic Embryos", 17(1): 9–16
Rosdianti, Ida, "Genomic Variation of Five Indonesian Cacao
(Theobroma cacao L.) Varieties Based on Analysis Using Next
Generation Sequencing", 17(2): 57–64
Rubiyo, "Genomic Variation of Five Indonesian Cacao (Theobroma
cacao L.) Varieties Based on Analysis Using Next Generation
Sequencing", 17(2): 57–64
S
Saleh, Norihan Mohamad, "Sensitivity of Pigment Content of Banana
and Orchid Tissue Culture Exposed to Extremely Low Frequency
Electromagnetic Field", 17(1): 27–34
Satyawan, Dani, "Genomic Variation of Five Indonesian Cacao
(Theobroma cacao L.) Varieties Based on Analysis Using Next
Generation Sequencing", 17(2): 57–64
Suk-Ha-Lee, "The Potential Use of SSR Markers to Support the
Morphological Identification of Indonesian Mungbean Varieties",
17(2): 65–74
Sumaryono, "Effect of Gamma Irradiation on The Growth and
Development of Sago Palm (Metroxylon sagu Rottb.) Calli",
17(1): 35–40
Sustiprijatno, "Agrobacterium tumefaciens-Mediated In-Planta
Transformation of Indonesian Maize Using plG121Hm-Cs
Plasmid Containing nptII and hpt Genes", 17(2): 49–56
Syahbuddin, Haris, "Production and Quality Enhancement of Mango
Using Fan Jet Sprayer Irrigation Technique", 17(2): 41–48
Syaufina, Lailan, "Capillary Water Rise in Peat Soil As Affected By
Various Groundwater Levels", 17(2): 75–83
8686-2 Indonesian Journal of Agricultural Science/Author Index
T
Tasma, I Made, "Genomic Variation of Five Indonesian Cacao
(Theobroma cacao L.) Varieties Based on Analysis Using Next
Generation Sequencing", 17(2): 57–64
Y
Yang, Tae-Jin, "Development of EST-SSR Markers to Assess Genetic
Diversity of Broccoli and Its Related Species", 17(1): 17–26
87
INDONESIAN JOURNAL OF AGRICULTURAL SCIENCE
Vol. 17, 2016
Subject Index
Indonesian Journal of Agricultural Science/Subject Index 87-1
Banana
Carotene 27
Chlorophyll 27
Electro-magnetic field 27
Orchid 27
Broccoli
Cauliflower 17
EST-SSR markers 17
Genetic diversity 17
Kohlrabi 17
Ferrous iron
Acid sulphate soil 1
Plant growth 1
Redox potential 1
Garcinia mangostana
Callus induction 9
Plant growth regulator 9
Somatic embryo 9
Maize
Agrobacterium tumefaciens 49
In-planta transformation 49
Mango
Fan jet sprayer 41
Production 41
Quality 41
Metroxylon sagu
Embryogenic calli 35
Gamma irradiation 35
Somatic embryo 35
Mungbean
DNA fingerprint 65
Morphological characters 65
SSR markers 65
Varietal identity 65
Peat soil
Bulk density 75
Capillary water 75
Groundwater level 75
Water content 75
Somatic embryo
Garcinia mangostana 9
Metroxylon sagu 35
Theobroma cacao
Genome sequencing 57
Genome variation 57
Next generation sequencing 57
SNP 57
88
ACKNOWLEDGEMENT OF REVIEWERS
The editorial staff of IJAS would like to acknowledge the scientists who reviewed articles published in 2016.
Their contributions ensure scientific quality of the publication.
Name Address Discipline
Prof. Ika Mariska Indonesian Center for Agricultural Plant Physiologi and
Biotechnology and Genetic Resources Biotechnology
Research and Development
Jalan Tentara Pelajar No. 3A
Bogor 16111, Indonesia
Dr. Backki Kim Texas A&M University, College Station, Biochemistry, Genetics and
TX 77843, United States Molecular Biology
Kularb Laosatit Faculty of Agriculture at Kamphaeng Saen, Genetic and Molecular
Kasetsart University, Kamphaeng Saen, Biology
Nakhon Pathom, 73140, Thailand
Dr. Sutoro Indonesian Center for Agricultural Agronomy
Biotechnology and Genetic Resources
Research and Development
Jalan Tentara Pelajar No. 3A
Bogor 16111, Indonesia
Dr. Made Jana Mejaya Indonesian Center for Food Crops Plant Breeding
Research and Development
Jalan Merdeka No. 147
Bogor 16111, Indonesia
Dr. Ahmad Kurnain Lambung Mangkurat University Soil Science
Banjarmasin, Indonesia
Prof. Purwiyatno Hariyadi Bogor Agricultural University Postharvest
IPB Dramaga Campus,
Bogor 16680, Indonesia
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Akhter, M. and C.H. Sneller. 1996. Yield and yield
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Anda, M, E.Suryani, Husnain, and D.Subardja. 2015.
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Sudaryono, A. Taufik, dan A. Wijanarko. 2007. Peluang
peningkatan produksi kedelai di Indonesia. hlm. 130–167.
Dalam Kedelai: Teknik produksi dan pengembangannya.
Sumarno, Suyamto, A. Widjono, Hermanto, dan H. Kasim
(Ed.). Pusat Penelitian dan Pengembangan Tanaman
Pangan, Bogor, Indonesia.
Dissertation/theses
Simpson, B.K. 1984. Isolation, Characterization, and Some
Application of Tripsin from Greenland Cod (Gadus
morhua). PhD Thesis. Memorial University of New-
foundland, St. John’s, Newfoundland, Canada. 179 pp.
Conference proceedings
Tangendjaja, B. and E. Wina. 2000. Tannins and ruminant
production in Indonesia. p. 40–43. In J.D. Brooker (Ed.)
Tannins in Livestock and Human Nutrition. Proceedings
of an International Workshop, Adelaide, Australia, 31
May–2 June 1999. ACIAR Proceedings No. 92.
Budi, D.S. 2000. Toleransi kedelai (Glycine max (L.) Merr.)
terhadap genangan air statis pada berbagai fase pertum-
buhan. hlm. 207–212. Dalam V.W. Gunawan, N. Sunarlin,
T. Handayani, B. Soegiarto, W. Adil, B. Priyanto, dan
Suwarno (Ed.). Prosiding Lokakarya Penelitian dan
Pengembangan Produksi Kedelai di Indonesia. Direktorat
Teknologi Lingkungan, Jakarta, Indonesia.
Conference paper
Chin, L.J., L.M. Tan, and K. Wegleitner. 2007. The occurrence
of mycotoxins in feed samples from Asia. A continuation
of the Bromin mycotoxin survey program. Paper presented
in 15th Annual ASA-IM Southeast Asian Feed Technology
and Nutrition Workshop, 27–30 May 2007, Bali-Indonesia.
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Heidhues, P. and B. Kassogi. 2005. The Impact of Consumer
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Research Discussion Paper 4849.
Article online
Hawk, A. 2004. Mycotoxins. Proc. Grain Elevator and
Processing Society (GEAPS). http://www.geaps.com/
proceedings/2004/Hawk.ctm. (1 July 2008).
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Husen, E., A.T. Wahyudi, A. Suwanto, and R. Saraswati.
2008. Prospective use of ACC deaminase-producing
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biotic and abiotic stresses in peat-soil-agriculture.
Microbiol. Indones. (in press).
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